Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models

Abstract

KRAS is the most commonly mutated oncogene, yet no effective targeted therapies exist for KRAS mutant cancers. We developed a pooled shRNA-drug screen strategy to identify genes that, when inhibited, cooperate with MEK inhibitors to effectively treat KRAS mutant cancer cells. The anti-apoptotic BH3 family gene BCL-XL emerged as a top hit through this approach. ABT-263 (navitoclax), a chemical inhibitor that blocks the ability of BCL-XL to bind and inhibit pro-apoptotic proteins, in combination with a MEK inhibitor led to dramatic apoptosis in many KRAS mutant cell lines from different tissue types. This combination caused marked in vivo tumor regressions in KRAS mutant xenografts and in a genetically engineered KRAS-driven lung cancer mouse model, supporting combined BCL-XL/MEK inhibition as a potential therapeutic approach for KRAS mutant cancers.

Figure 1. Identification of BCL-XL as a Potential Target for Combination Therapy with MEK Inhibitors in KRAS Mutant Cancers

(A) Schematic of the pooled shRNA-drug screen approach. 1: Target cells are infected with a pooled lentiviral shRNA library. 2 and 3: Cells are aliquoted into three parts: one part is immediately frozen to represent the initial population, and the other two parts are treated with vehicle or 1 µM selumetinib (SEL) for 7 days. 4 and 5: Genomic DNA is isolated from cells, lentiviral cassettes are PCR-amplified, and individual shRNA abundance is quantified by deep sequencing. (B) Western blot of cells infected with shRNAs targeting GFP or BCL-XL and lysates. (C) Cells were infected with the indicated shRNAs. Following 48-hr puromycin selection, cells were cultured with or without 1 µM SEL for an additional 72 hr and stained with crystal violet. (D) Quantification of crystal violet staining from cells in (C). Error bars represent SEM. See also Figure S1 and Tables S1 and S2.

Figure 2. Pharmacologic Inhibition of BCL-XL and MEK in KRAS Mutant Cancer Cells

(A) Cells were treated with vehicle (Control), 1 µM ABT-263 (ABT), 1 µM selumetinib (SEL), or the combination for 72 hr. Values represent the change in viable cell number relative to starting cell titer immediately before treatment. p < 0.01(*) or < 0.001(**) for ABT/SEL versus all other groups by one-way ANOVA with Tukey post-hoc test. (B) Cells were treated as in (A) for 72 hr and the percentage of apoptotic cells was determined by Annexin V staining. All error bars represent SEM. (C) Western blot of cells treated with ABT, SEL, or the combination for 24 hr. (D) Cells were treated for 24 hr with ABT, SEL, or the combination. Left, immunoprecipitation was performed with immunoglobulin G control antibody or anti-BIM antibody, and the immunoprecipitate was probed with the indicated antibodies. Right, pre-immunoprecipitation lysates (L) and supernatants (S) following immunoprecipitation with anti-BIM antibody were probed with the indicated antibodies. (E) Thirty KRAS mutant cell lines were treated with ABT, SEL, or the combination for 72 hr and the percentage of apoptotic cells was determined by Annexin V staining. For each cell line, the percent apoptosis is color-coded by quartile. (F) The percentage of all cell lines exhibiting the indicated degree of apoptosis is shown. See also Figure S2 and Table S3.

Figure 3. Epithelial Differentiation Predicts Sensitivity to the Combination of ABT-263 and Selumetinib

(A) Heat map showing the top genes differentially expressed according to sensitivity to ABT-263/selumetinib as generated by the PAMR algorithm utilizing gene expression profiles from the KRAS mutant cell line panel. Red arrows represent genes that are upregulated and blue arrows represent genes that are down-regulated in a previously reported EMT gene signature. Vimentin (VIM) and E-cadherin (CDH1), markers of mesenchymal and epithelial differentiation, respectively, are indicated. (B and C) Correlation of apoptosis induced by ABT-263/selumetinib with (B) a KRAS dependency gene signature and (C) E-cadherin protein expression. Each dot represents a single cell line. P values were generated by two-tailed t test. (D) Western blot of A549 cells infected with shRNA targeting GFP (shGFP) or Zeb1 (shZeb1). (E) A549 cells infected with shGFP or shZeb1 were treated with vehicle (CON), 1 µM ABT-263 (ABT), 1 µM selumetinib (SEL), or the combination for 72 hr. Values represent the change in viable cell number relative to starting cell titer immediately before treatment. The p values were determined by one-way ANOVA with Tukey post-hoc test. All error bars represent SEM. See also Figure S3 and Table S4.

Figure 4. In Vivo Efficacy of Combined BCL-XL and MEK Inhibition

(A) KRAS mutant xenografts were treated with vehicle (CON), ABT-263 (ABT, 100 mg/kg daily), selumetinib (SEL, 25 mg/kg twice daily), or both drugs in combination. The mean percent change in tumor volume relative to initial tumor volume is shown. Error bars represent SEM. (B) Waterfall plot showing the percent change in tumor volume (relative to initial volume) for individual tumors in the SEL and ABT/SEL groups following 21 days of treatment. P values were generated by two-tailed t test. (C) Tumor tissue from HCT116 xenografts treated for 3 days with the indicated drug regimens was evaluated by immunohistochemistry for P-ERK, Ki67 (a marker of proliferation), or cleaved caspase 3 (a marker of apoptosis). Tumors were harvested 3 hr after dosing on day 3. Scale bar represents 100 µm. (D and E) Established lung tumors in LSL-KRAS^G12D mice were treated with vehicle, ABT, SEL, or both drugs in combination as in (A). (D) MR images of two mice obtained pretreatment and following 1 week of treatment with the ABT/SEL combination. Red arrows indicate dense areas of lung tumor in the pretreatment images. (E) Mean percent tumor regression of lung tumors following 2 weeks of the indicated treatment. p represents ABT/SEL versus each treatment group by one-way ANOVA with Tukey post-hoc test. All error bars represent SEM. See also Figure S4.